CAS Array:design and assessment of a genotyping array for Chinese biobanking  

作　　者：Zijian Tian Fei Chen Jing Wang Benrui Wu Jian Shao Ziqing Liu Li Zheng You Wang Tao Xu Kaixin Zhou 

机构地区：[1]National Laboratory of Biomacromolecules,Institute of Biophysics Chinese Academy of Sciences,Beijing 100101,China [2]College of Life Sciences,University of the Chinese Academy of Sciences,Beijing 10140,China [3]Department of Mathematics and Interdisciplinary,Guangzhou Laboratory,Guangzhou 510005,China [4]College of Public Health,Guangzhou Medical University,Guangzhou 510006,China

出　　处：《Precision Clinical Medicine》2023年第1期1-7,共7页精准临床医学（英文）

基　　金：supported by the National Key R&D Program of China(Grant No.2018YFC2001003);the Strategic Priority Research Program of the Chinese Academy of Sciences(category B,Grant No.XDB38020100).

摘　　要：Background:Chronic diseases are becoming a critical challenge to the aging Chinese population.Biobanks with extensive genomic and environmental data offer opportunities to elucidate the complex gene-environment interactions underlying their aetiology.Genome-wide genotyping array remains an efficient approach for large-scale genomic data collection.However,most commercial arrays have reduced performance for biobanking in the Chinese population.Materials and methods:Deep whole-genome sequencing data from 2641 Chinese individuals were used as a reference to develop the CAS array,a custom-designed genotyping array for precision medicine.Evaluation of the array was performed by comparing data from 384 individuals assayed both by the array and whole-genome sequencing.Validation of its mitochondrial copy number estimating capacity was conducted by examining its association with established covariates among 10162 Chinese elderly.Results:The CAS Array adopts the proven Axiom technology and is restricted to 652429 single-nucleotide polymorphism(SNP)markers.Its call rate of 99.79% and concordance rate of 99.89% are both higher than for commercial arrays.Its imputation-based genome coverage reached 98.3% for common SNPs and 63.0% for low-frequency SNPs,both comparable to commercial arrays with larger SNP capacity.After validating its mitochondrial copy number estimates,we developed a publicly available software tool to facilitate the array utility.Conclusion:Based on recent advances in genomic science,we designed and implemented a high-throughput and low-cost genotyping array.It is more cost-effective than commercial arrays for large-scale Chinese biobanking.

关 键 词：GENOTYPING single-nucleotide polymorphism(SNP) mitochondrial copy number chronic disease precision medicine SNP array 

分 类 号：Q78[生物学—分子生物学]